bulk-rnaseq
From the author
This skill should be used when running bulk RNA-seq differential expression analysis: FastQC/trimming, Salmon quantification, counts matrix construction, DESeq2 statistics, GO/KEGG enrichment and publication figures. 用于 bulk 转录组（RNA-seq）差异表达分析全流程。
Install
npx skills add ssinder/bioinformatics-agent-skills --skill bulk-rnaseq -a claude-code
Installs to .claude/skills/bulk-rnaseq/ · Each command fetches the skill straight from GitHub with the open skills CLI.
Byte-identical to the scanned commit, with the repository’s licence and a SOURCE.txt.
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Why 76
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Similar skills
Closest to this one by what they do and when they are used.
- single-cell-rnaseqssinder/bioinformatics-agent-skillsThis skill should be used when running single-cell RNA-seq analysis: reading 10x/AnnData matrices, QC filtering, normalization, HVG selection, PCA, clustering, UMAP/t-SNE and cell type annotation. 用于单细胞转录组（scRNA-seq）质控、降维、聚类与细胞注释全流程。Other★ 75
- rna-seq-analysisawslabs/hcls-agent-skillsBulk RNA-seq analysis pipeline covering alignment (STAR), quantification (Salmon, featureCounts), and differential expression (DESeq2). Triggers on RNA-seq, STAR, Salmon, DESeq2, differential expression, gene expression, tximport, featureCounts, transcriptomics, "bulk RNA-seq", "STAR alignment", "Salmon quantification", "gene counts", "DESeq2 results", "shrinkage estimator", "volcano plot RNA-seq".Other★ 71
- rnaseq-deComeOnOliver/skillshubDifferential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.Testing★ 65
- pydeseq2K-Dense-AI/scientific-agent-skillsPerforms bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage, and result visualization. Use for PyDESeq2 or Python DESeq2 workflows with biological replicates.Testing★ 56K
- alterlab-pydeseq2AlterLab-IEU/AlterLab-Academic-SkillsRun differential gene expression analysis on bulk RNA-seq count matrices with PyDESeq2, the Python port of DESeq2 — size-factor normalization, dispersion estimation, Wald tests, FDR (Benjamini-Hochberg) correction, and volcano/MA plots. Use when identifying differentially expressed genes between conditions from raw bulk RNA-seq counts. Part of the AlterLab Academic Skills suite.Testing★ 84
- alterlab-rnaseq-quantAlterLab-IEU/AlterLab-Academic-SkillsQuantifies bulk RNA-seq transcript abundance with salmon 2.x (the Rust rewrite; selective alignment or --sketch) and kallisto (v0.52.0, kb-python workflow), builds a decoy-aware gentrome index, runs quant with --gcBias -l A, then imports estimates via tximport/tximeta with a tx2gene map and hands differential expression to alterlab-pydeseq2. Warns that salmon 2.0 cannot read C++/pufferfish indices (rebuild every index), that --validateMappings is now accepted-but-ignored, and that 'salmon alevin' was REMOVED (single-cell now uses piscem + alevin-fry). Use when quantifying RNA-seq transcript abundance, running salmon or kallisto, building a decoy-aware index, or wiring tximport to DESeq2; for differential expression use alterlab-pydeseq2, for FASTQ-to-VCF variant calling use alterlab-nf-core-sarek. Part of the AlterLab Academic Skills suite.Engineering★ 84
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